A bone implant and a manufacturing method thereof are provided. The bone implant is used for implanting a bone of a living body, such as bone, vertebra and alveolar bone. The bone implant includes an implanting body and a plurality of microstructures formed on a surface of the implanting body. An inner layer of the bone implanting body is made of metal including titanium or alloy including titanium, and an outer layer of the bone implanting body is titanium dioxide. Each microstructure has a height and a width, wherein the width is less than 2 micrometers and the height is less than 1 micrometer.